EMILIN2 p.Pro901=
c.2703G>A · rs147900182 · VCV2648522
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0604%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.8 | |
| Overall | ||
| CADD | 0.482 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0604%
South Asian · 55/91,080 alleles
Filtering AF
0.0563%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0547%
Overall
0.0512%
827/1,613,926 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0604% | 1,656 |
| European (non-Finnish) | 0.0599% | 1,669 |
| Middle Eastern | 0.0495% | 2,019 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| Finnishnot grpmax-eligible | 0.0344% | 2,911 |
| Admixed American | 0.0167% | 6,000 |
| African / African-American | 0.00933% | 10,720 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- EMILIN2
- Protein
- p.Pro901=
- Coding
- c.2703G>A
- MANE Select
- NM_032048
- dbSNP
- rs147900182
- Type
- single nucleotide variant
- Location
- chr18:2909698 (GRCh38)
- Gene constraint
- LOEUF 1.047 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.88
- Residue 901
- the c1q domain; the 'disordered' region
Similar variants
- EMILIN2 p.Ala215Thr Benign ★★ same type
- EMILIN2 p.Ala455= Benign ★★ same type
- EMILIN2 p.Cys1002= Benign ★★ same type
- EMILIN2 p.Gly843= Benign/Likely benign ★★ same type
- EMILIN2 p.Lys347= Benign ★★ same type
- EMILIN2 p.Met259Val Benign ★★ same type
- EMILIN2 p.Pro136Ser Benign ★★ same type
- EMILIN2 p.Pro657= Benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/emilin2-p-pro901 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown